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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Related Experiment Video

Updated: Apr 26, 2026

mirMachine: A One-Stop Shop for Plant miRNA Annotation

mirMachine: A One-Stop Shop for Plant miRNA Annotation

Published on: May 1, 2021

miRSeq: a user-friendly standalone toolkit for sequencing quality evaluation and miRNA profiling.

Cheng-Tsung Pan¹, Kuo-Wang Tsai², Tzu-Min Hung³

¹Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.

Biomed Research International

|August 13, 2014

Summary

miRSeq offers a user-friendly solution for analyzing small RNA next-generation sequencing (NGS) data. This standalone toolkit precisely evaluates sequencing quality and provides miRNA expression profiles for over 100 species.

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Last Updated: Apr 26, 2026

mirMachine: A One-Stop Shop for Plant miRNA Annotation

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Published on: May 1, 2021

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs

Published on: September 16, 2019

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools

Published on: August 21, 2019

Area of Science:

Molecular Biology
Bioinformatics

Background:

MicroRNAs (miRNAs) are crucial regulators of biological processes.
Analyzing miRNA expression profiles typically involves next-generation sequencing (NGS).
Existing online tools for small RNA NGS data analysis face challenges with data submission, format conversion, and species limitations.

Purpose of the Study:

To develop an alternative solution for small RNA NGS data analysis.
To introduce miRSeq, a user-friendly standalone toolkit.
To address limitations of current web services for miRNA analysis.

Main Methods:

Developed miRSeq, a standalone toolkit with a graphical user interface (GUI).
Analyzed small RNA NGS data from human, rat, fly, and nematode using miRSeq.
Evaluated sequencing quality metrics including self-ligation read percentage, read length distribution, and read category.

Main Results:

miRSeq precisely evaluates sequencing quality of small RNA NGS samples.
The toolkit provides miRNA expression profiles, 3' end modification patterns, and isomiR forms.
miRSeq supports the analysis of up to 105 animal species, offering enhanced flexibility.

Conclusions:

miRSeq provides a precise and user-friendly alternative for small RNA NGS data analysis.
The toolkit simplifies the process of obtaining valuable miRNA expression data.
miRSeq's broad species support enhances its utility for diverse research applications.